Water hyacinth (Eichhornia crassipes) causes environmental, agricultural and health problems in Mali. This is particularly severe in the District of Bamako and the irrigation systems of the “Office du Niger” area. During two years survey for fungal pathogens of water hyacinth infested areas, isolate Mlb684 was collected from diseased plant. This fungal isolate was identified as a potential mycoherbicide for sustainable management for water hyacinth. The aim of this study was to characterize isolate Mlb684. The characterization was based on a morphological description and a DNA sequence analysis. Various genes amplified from isolate Mlb684 were compared to those existing in Genbank. These genes were 18S ribosomal rDNA gene, ITS rDNA gene, elongation factor-1 alpha (EF1a) gene, calmodulin and actin genes. DNA sequence comparisons and morphological description provided enough evidences to show that isolate Mlb684 belonged to the Alternaria genus and was distinct from any other known Alternaria species. Based on these evidences, the new fungal isolate was called “Alternaria jacinthicola Dagno & M.H. Jijakli”. A specimen culture has been deposited in the Gembloux Agro Bio Tech Plant Pathology unit fungal collection, with Mlb684 reference and in the Industrial Fungal and Yeast Collection (BCCM/MUCL, Belgium) under the accession number: MUCL 53159 and all DNA sequences were deposited in GenBank (NCBI).